
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   25 (  100),  selected   25 , name T0320TS550_2_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS550_2_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    E     248      N     228          2.824
LGA    W     249      N     229          3.451
LGA    E     250      S     230          3.504
LGA    I     251      L     231          3.090
LGA    I     252      P     232          1.289
LGA    H     253      N     233          3.054
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    A     254      R     237          2.267
LGA    F     255      K     238          2.998
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    G     256      N     242          4.139
LGA    K     257      P     243          4.375
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    D     258      G     290          2.651
LGA    A     259      W     291          2.758
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    E     260      V     294          3.102
LGA    G     261      D     295           #
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    E     262      E     299          1.905
LGA    R     263      R     300          3.563
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    S     264      R     303          1.836
LGA    S     265      I     304          3.392
LGA    A     266      -       -           -
LGA    I     267      -       -           -
LGA    N     268      -       -           -
LGA    T     269      -       -           -
LGA    S     270      -       -           -
LGA    P     271      -       -           -
LGA    I     272      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   73    5.0     17    3.05    11.76     14.052     0.539

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.212161 * X  +  -0.660659 * Y  +  -0.720082 * Z  +  14.439226
  Y_new =   0.417097 * X  +  -0.605150 * Y  +   0.678102 * Z  +  -6.724660
  Z_new =  -0.883752 * X  +  -0.444211 * Y  +   0.147170 * Z  +   7.574198 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.250871    1.890722  [ DEG:   -71.6696    108.3304 ]
  Theta =   1.083820    2.057772  [ DEG:    62.0983    117.9017 ]
  Phi   =   1.100245   -2.041348  [ DEG:    63.0394   -116.9606 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0320TS550_2_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS550_2_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   73   5.0   17   3.05   11.76  14.052
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS550_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1mkn_A
ATOM      1  N   GLU   248      28.497  21.694   9.720  1.00  0.00
ATOM      2  CA  GLU   248      28.699  20.605   8.720  1.00  0.00
ATOM      3  C   GLU   248      27.551  19.615   8.915  1.00  0.00
ATOM      4  O   GLU   248      27.641  18.717   9.717  1.00  0.00
ATOM      5  N   TRP   249      26.443  19.807   8.250  1.00  0.00
ATOM      6  CA  TRP   249      25.272  18.904   8.486  1.00  0.00
ATOM      7  C   TRP   249      25.147  17.853   7.379  1.00  0.00
ATOM      8  O   TRP   249      24.644  18.122   6.307  1.00  0.00
ATOM      9  N   GLU   250      25.573  16.643   7.647  1.00  0.00
ATOM     10  CA  GLU   250      25.440  15.566   6.623  1.00  0.00
ATOM     11  C   GLU   250      23.956  15.429   6.296  1.00  0.00
ATOM     12  O   GLU   250      23.135  15.959   7.009  1.00  0.00
ATOM     13  N   ILE   251      23.429  15.328   5.179  1.00  0.00
ATOM     14  CA  ILE   251      22.943  15.490   3.820  1.00  0.00
ATOM     15  C   ILE   251      21.437  15.597   3.908  1.00  0.00
ATOM     16  O   ILE   251      20.816  14.855   4.658  1.00  0.00
ATOM     17  N   ILE   252      20.851  16.514   3.143  1.00  0.00
ATOM     18  CA  ILE   252      19.407  16.727   3.171  1.00  0.00
ATOM     19  C   ILE   252      18.602  15.760   2.283  1.00  0.00
ATOM     20  O   ILE   252      18.741  15.760   1.057  1.00  0.00
ATOM     21  N   HIS   253      17.751  14.951   2.917  1.00  0.00
ATOM     22  CA  HIS   253      16.915  13.975   2.216  1.00  0.00
ATOM     23  C   HIS   253      15.803  14.687   1.445  1.00  0.00
ATOM     24  O   HIS   253      15.057  15.491   2.003  1.00  0.00
ATOM     25  N   ALA   254      15.688  14.365   0.163  1.00  0.00
ATOM     26  CA  ALA   254      14.704  14.996  -0.697  1.00  0.00
ATOM     27  C   ALA   254      13.452  14.164  -0.962  1.00  0.00
ATOM     28  O   ALA   254      12.572  14.584  -1.714  1.00  0.00
ATOM     29  N   PHE   255      13.376  12.981  -0.363  1.00  0.00
ATOM     30  CA  PHE   255      12.204  12.129  -0.540  1.00  0.00
ATOM     31  C   PHE   255      11.638  11.765   0.828  1.00  0.00
ATOM     32  O   PHE   255      12.355  11.779   1.831  1.00  0.00
ATOM     33  N   GLY   256      10.353  11.442   0.861  1.00  0.00
ATOM     34  CA  GLY   256       9.718  11.085   2.114  1.00  0.00
ATOM     35  C   GLY   256       9.297  12.286   2.943  1.00  0.00
ATOM     36  O   GLY   256       9.252  13.415   2.451  1.00  0.00
ATOM     37  N   LYS   257       8.984  12.035   4.212  1.00  0.00
ATOM     38  CA  LYS   257       8.566  13.088   5.115  1.00  0.00
ATOM     39  C   LYS   257       9.796  13.659   5.809  1.00  0.00
ATOM     40  O   LYS   257      10.547  12.939   6.471  1.00  0.00
ATOM     41  N   ASP   258      10.017  14.974   5.661  1.00  0.00
ATOM     42  CA  ASP   258      11.150  15.694   6.250  1.00  0.00
ATOM     43  C   ASP   258      11.210  15.530   7.758  1.00  0.00
ATOM     44  O   ASP   258      12.277  15.626   8.358  1.00  0.00
ATOM     45  N   ALA   259      10.054  15.302   8.367  1.00  0.00
ATOM     46  CA  ALA   259       9.982  15.141   9.811  1.00  0.00
ATOM     47  C   ALA   259      10.648  13.842  10.236  1.00  0.00
ATOM     48  O   ALA   259      11.267  13.764  11.302  1.00  0.00
ATOM     49  N   GLU   260      10.527  12.829   9.386  1.00  0.00
ATOM     50  CA  GLU   260      11.112  11.527   9.663  1.00  0.00
ATOM     51  C   GLU   260      12.597  11.455   9.267  1.00  0.00
ATOM     52  O   GLU   260      13.261  10.435   9.463  1.00  0.00
ATOM     53  N   GLY   261      13.113  12.552   8.724  1.00  0.00
ATOM     54  CA  GLY   261      14.509  12.630   8.320  1.00  0.00
ATOM     55  C   GLY   261      15.338  13.071   9.532  1.00  0.00
ATOM     56  O   GLY   261      14.851  13.814  10.383  1.00  0.00
ATOM     57  N   GLU   262      16.580  12.598   9.615  1.00  0.00
ATOM     58  CA  GLU   262      17.482  12.930  10.724  1.00  0.00
ATOM     59  C   GLU   262      18.924  13.033  10.216  1.00  0.00
ATOM     60  O   GLU   262      19.647  12.038  10.171  1.00  0.00
ATOM     61  N   ARG   263      19.526  14.362   9.660  1.00  0.00
ATOM     62  CA  ARG   263      20.887  14.544   9.097  1.00  0.00
ATOM     63  C   ARG   263      21.853  14.416  10.265  1.00  0.00
ATOM     64  O   ARG   263      21.440  14.168  11.380  1.00  0.00
ATOM     65  N   SER   264      23.127  14.554  10.054  1.00  0.00
ATOM     66  CA  SER   264      24.040  14.400  11.218  1.00  0.00
ATOM     67  C   SER   264      25.403  15.017  10.931  1.00  0.00
ATOM     68  O   SER   264      25.975  14.793   9.882  1.00  0.00
ATOM     69  N   SER   265      25.954  15.784  11.843  1.00  0.00
ATOM     70  CA  SER   265      27.290  16.354  11.539  1.00  0.00
ATOM     71  C   SER   265      27.913  17.089  12.720  1.00  0.00
ATOM     72  O   SER   265      27.850  16.654  13.849  1.00  0.00
ATOM     73  N   ALA   266      28.574  18.182  12.439  1.00  0.00
ATOM     74  CA  ALA   266      29.275  18.938  13.508  1.00  0.00
ATOM     75  C   ALA   266      29.155  20.447  13.277  1.00  0.00
ATOM     76  O   ALA   266      28.946  20.902  12.175  1.00  0.00
ATOM     77  N   ILE   267      28.772  20.763  14.539  1.00  0.00
ATOM     78  CA  ILE   267      27.491  20.980  15.224  1.00  0.00
ATOM     79  C   ILE   267      26.305  20.032  14.991  1.00  0.00
ATOM     80  O   ILE   267      25.909  19.306  15.905  1.00  0.00
ATOM     81  N   ASN   268      25.733  20.053  13.785  1.00  0.00
ATOM     82  CA  ASN   268      24.567  19.224  13.452  1.00  0.00
ATOM     83  C   ASN   268      24.710  17.734  13.746  1.00  0.00
ATOM     84  O   ASN   268      23.707  17.047  13.945  1.00  0.00
ATOM     85  N   THR   269      25.955  17.257  13.778  1.00  0.00
ATOM     86  CA  THR   269      26.299  15.850  14.041  1.00  0.00
ATOM     87  C   THR   269      25.314  15.094  14.933  1.00  0.00
ATOM     88  O   THR   269      24.715  14.105  14.512  1.00  0.00
ATOM     89  N   SER   270      25.818  15.972  16.274  1.00  0.00
ATOM     90  CA  SER   270      24.604  15.174  16.627  1.00  0.00
ATOM     91  C   SER   270      23.695  15.031  15.415  1.00  0.00
ATOM     92  O   SER   270      24.084  15.300  14.295  1.00  0.00
ATOM     93  N   PRO   271      22.486  14.587  15.626  1.00  0.00
ATOM     94  CA  PRO   271      21.561  14.404  14.485  1.00  0.00
ATOM     95  C   PRO   271      20.263  15.166  14.729  1.00  0.00
ATOM     96  O   PRO   271      19.929  15.540  15.836  1.00  0.00
ATOM     97  N   ILE   272      19.535  15.374  13.677  1.00  0.00
ATOM     98  CA  ILE   272      18.230  16.094  13.741  1.00  0.00
ATOM     99  C   ILE   272      17.392  15.556  12.624  1.00  0.00
ATOM    100  O   ILE   272      17.876  15.326  11.553  1.00  0.00
TER
END
